Hi,
I have 2 RnaSeq fq files that i need to analyze.i did the quality trimming and adapter trimming for the files as they were need to do it
then i got 2 output files that are 1.fq file(36 million bp reads) and 2.fq(40 million bp reads) with length of 20-36bp reads in it
I used tophat for aligning them to reference.then when i ran the tophat it is saying to decrease the --segment-length to half of the read length.
do i need to give the --segment-length to 18?or run with the default 25?
i need help in --coverage-search( when i used it in default it was saying that th e tophat will work slow if i used it)do i need to use the --no-coverage-search option for this?does it have any difference?
Please help me i am new in using the tophat
Thank you
I have 2 RnaSeq fq files that i need to analyze.i did the quality trimming and adapter trimming for the files as they were need to do it
then i got 2 output files that are 1.fq file(36 million bp reads) and 2.fq(40 million bp reads) with length of 20-36bp reads in it
I used tophat for aligning them to reference.then when i ran the tophat it is saying to decrease the --segment-length to half of the read length.
do i need to give the --segment-length to 18?or run with the default 25?
i need help in --coverage-search( when i used it in default it was saying that th e tophat will work slow if i used it)do i need to use the --no-coverage-search option for this?does it have any difference?
Please help me i am new in using the tophat
Thank you